rule all:
    input:
        expand("{sample}.sorted.markdup.bam", sample=config["sample"]),
        expand("{sample}.sorted.markdup.bai", sample=config["sample"]),
        expand("{sample}.gvcf.gz", sample=config["sample"]),
        expand("{sample}.gvcf.gz.tbi", sample=config["sample"]),
        expand("{sample}.snv.vcf.gz", sample=config["sample"]),
        expand("{sample}.snv.vcf.gz.tbi", sample=config["sample"])

include: "rules/bam2gvcf.smk"
include: "rules/gvcf2vcf.smk"